what does mean by index "1" in predicted motif: motif1by meme

[raghvendra singh]

Dear Sir/Maám,

I used meme offline version for analysis.

my query is:

what is the criteria to signed indexes for each predicted motifs, like 1  motif 1 , motif2, motif3....... motif10.

what is the logic behind the assigning these numbers.

I checked it for Log Likelihood Ratio, Information Content, Relative Entropy, Bayes Threshold it does not based on these parameters.

​waiting for your kind response​

[James Johnson]

MEME attempts to find the best motifs first (as measured by E-value where smaller is better) however due to the nature of the algorithm it has to make a lot of guesses about what will be the best starting point for creating a motif. As there is quite a lot of work done between picking a starting point and calculating the E-value it does not always succeed and so the ordering is not based on any specific output measurement but rather which starting point looked most promising.

The number assigned is simply the order that MEME found the motifs.